American Floyd Landis finished fourth and reclaimed the overall lead in cycling's most prestigious event.
Schleck completed Tuesday's 187-kilometer mountain stage from Gap to L'Alpe-d'Huez in a time of 4 hours, 52 minutes and 22 seconds, beating Italy's Damiano Cunego by 11 seconds.
Stefano Garzelli of Italy was third, 1:10 behind, while Landis and Germany's Andreas Kloden rounded out the top five with the same time.
Landis, who held the overall lead for two days last week, started the day 1:29 behind overall leader Oscar Pereiro of Spain. Pereiro was among a group behind Landis and could only manage a 14th-place finish on Tuesday, 2:49 off the lead pace. He is now second overall, 10 seconds behind Landis.